{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:55:28Z","timestamp":1762865728925},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2151,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the \u2018uniqueome\u2019, a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data.<\/jats:p>\n               <jats:p>Availability: Files, scripts and supplementary data are available from http:\/\/grimmond.imb.uq.edu.au\/uniqueome\/; the ISAS uniqueome aligner is freely available from http:\/\/www.imagenix.com\/.<\/jats:p>\n               <jats:p>Contact: \u00a0n.cloonan@uq.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq640","type":"journal-article","created":{"date-parts":[[2010,11,13]],"date-time":"2010-11-13T01:20:02Z","timestamp":1289611202000},"page":"272-274","source":"Crossref","is-referenced-by-count":60,"title":["The uniqueome: a mappability resource for short-tag sequencing"],"prefix":"10.1093","volume":"27","author":[{"given":"Ryan","family":"Koehler","sequence":"first","affiliation":[{"name":"1 VerdAscend Sciences, West Linn, OR 97068, 2Imagenix Technologies, 2672 Bayshore Parkway Suite 502, Mountain View, CA 94043, USA and 3Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia"}]},{"given":"Hadar","family":"Issac","sequence":"additional","affiliation":[{"name":"1 VerdAscend Sciences, West Linn, OR 97068, 2Imagenix Technologies, 2672 Bayshore Parkway Suite 502, Mountain View, CA 94043, USA and 3Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia"}]},{"given":"Nicole","family":"Cloonan","sequence":"additional","affiliation":[{"name":"1 VerdAscend Sciences, West Linn, OR 97068, 2Imagenix Technologies, 2672 Bayshore Parkway Suite 502, Mountain View, CA 94043, USA and 3Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia"}]},{"given":"Sean M.","family":"Grimmond","sequence":"additional","affiliation":[{"name":"1 VerdAscend Sciences, West Linn, OR 97068, 2Imagenix Technologies, 2672 Bayshore Parkway Suite 502, Mountain View, CA 94043, USA and 3Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia"}]}],"member":"286","published-online":{"date-parts":[[2010,11,12]]},"reference":[{"key":"2023012512180566800_B1","doi-asserted-by":"crossref","first-page":"R62","DOI":"10.1186\/gb-2010-11-6-r62","article-title":"Whole exome capture in solution with 3 Gbp of data","volume":"11","author":"Bainbridge","year":"2010","journal-title":"Genome Biol."},{"key":"2023012512180566800_B2","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/ng.128","article-title":"Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing","volume":"40","author":"Campbell","year":"2008","journal-title":"Nat. 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Biotechnol."},{"key":"2023012512180566800_B7","doi-asserted-by":"crossref","first-page":"D755","DOI":"10.1093\/nar\/gkn875","article-title":"The UCSC Genome Browser Database: update 2009","volume":"37","author":"Kuhn","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512180566800_B8","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512180566800_B9","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.1101\/gr.078519.108","article-title":"Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding","volume":"18","author":"Robertson","year":"2008","journal-title":"Genome Res."},{"key":"2023012512180566800_B10","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/nbt.1518","article-title":"PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls","volume":"27","author":"Rozowsky","year":"2009","journal-title":"Nat. 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Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/272\/48869551\/bioinformatics_27_2_272.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/272\/48869551\/bioinformatics_27_2_272.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:56:56Z","timestamp":1674658616000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/2\/272\/285818"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,11,12]]},"references-count":12,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2011,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq640","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,1,15]]},"published":{"date-parts":[[2010,11,12]]}}}